Runtime Environment Contracts

A runtime environment contract identifies the tools, tracked inputs, and external dependencies required to reopen one shipped lane. Unsupported combinations are present claim refusals, not an informal roadmap.

flowchart LR
    T["required tools"] --> E["declared environment"]
    I["tracked inputs"] --> E
    D["external dependencies"] --> E
    E --> S["supported combinations"]
    E --> U["unsupported combinations"]

Qualify an environment

Decision	Evidence to inspect	Refusal condition
identify the lane	workflow family, runtime package ID, execution mode, and benchmark manifest	the request does not match one governed lane
resolve required tools	tool name, version, configuration, and availability	a required tool or declared capability is absent
bind tracked inputs	source paths, digests, schema identities, and benchmark revision	an input is missing, mutable, or does not match the retained contract
disclose external dependencies	imported engine outputs, remote services, credentials, licenses, and network assumptions	an external dependency is implicit or cannot be reconstructed
compare the supported envelope	operating system, Python and package versions, extras, providers, and checked combinations	the requested combination lies outside retained evidence
execute invalidation cases	unavailable provider, changed input, incompatible schema, missing artifact, and other lane-specific challenges	a challenged condition succeeds silently or produces an ambiguous result

Contract Fields

field	interpretation
required tools	minimum repository-owned execution lane
external dependencies	systems or imported evidence outside that lane
supported combinations	environment combinations defended by retained evidence
unsupported combinations	stronger combinations the current release refuses

Family Contracts

dda

• runtime package id: dda-maxquant-pipeline-corpus
• required tools: python 3.11, uv, bijux-proteomics-runtime, tracked public benchmark package files
• external dependencies: tracked exported results from maxquant 19.0, no live external engine install is required for the shipped rerun lane
• supported combinations: repository-managed python environment plus tracked imported benchmark exports
• unsupported combinations: claiming live external-engine parity from the shipped import lane, claiming raw instrument-side rerun without new tracked inputs and runtime support

dia

• runtime package id: dia-diann-pipeline-corpus
• required tools: python 3.11, uv, bijux-proteomics-runtime, tracked public benchmark package files
• external dependencies: none beyond tracked repository inputs
• supported combinations: repository-managed python environment plus tracked DIA report and comparator exports, library-conditioned review over the shipped benchmark package
• unsupported combinations: claiming chromatogram-native or vendor-parity DIA authority, treating library-conditioned exported reports as a substitute for raw acquisition replay

lfq

• runtime package id: lfq-cohort-review-corpus
• required tools: python 3.11, uv, bijux-proteomics-runtime, tracked public benchmark package files
• external dependencies: none beyond tracked repository inputs
• supported combinations: repository-managed python environment plus tracked benchmark package inputs
• unsupported combinations: claiming broader family authority than the shipped benchmark package and downstream consequence surfaces earn

multiplex

• runtime package id: multiplex-tmtpro-review-corpus
• required tools: python 3.11, uv, bijux-proteomics-runtime, tracked public benchmark package files
• external dependencies: none beyond tracked repository inputs
• supported combinations: repository-managed python environment plus tracked benchmark package inputs
• unsupported combinations: claiming outsider-auditable multiplex authority from the current internal-support lane

ptm

• runtime package id: ptm-localization-review-corpus
• required tools: python 3.11, uv, bijux-proteomics-runtime, tracked public benchmark package files
• external dependencies: none beyond tracked repository inputs
• supported combinations: repository-managed python environment plus tracked benchmark package inputs
• unsupported combinations: claiming broader family authority than the shipped benchmark package and downstream consequence surfaces earn

targeted

• runtime package id: targeted-transition-review-corpus
• required tools: python 3.11, uv, bijux-proteomics-runtime, tracked public benchmark package files
• external dependencies: none beyond tracked repository inputs
• supported combinations: repository-managed python environment plus tracked benchmark package inputs
• unsupported combinations: claiming broader family authority than the shipped benchmark package and downstream consequence surfaces earn

Review Rule

An environment claim may expand only when required tools, external dependencies, replay evidence, and failure behavior expand together. A green repository execution lane does not erase the unsupported combinations listed for that family.

Record the qualification

A reviewable environment decision retains the workflow family, runtime package ID, request fingerprint, input inventory, required and observed tool versions, package lock or environment identity, external dependencies, provider decisions, invalidation results, and final disposition.

Disposition	Meaning	Operator response
qualified	the exact declared combination is backed by retained replay evidence	proceed and bind the environment record to the run
degraded	execution is possible but one non-blocking environmental property differs	record the difference and keep claims inside the reviewed envelope
unsupported	the combination lies outside the retained contract	refuse the stronger environment claim; select a supported lane or add evidence
irreproducible	required inputs, tools, or external dependencies cannot be reconstructed	stop replay and preserve the missing dependency as the blocker